Ccl20 C-C motif chemokine ligand 20 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ccl20provided by RGD
Official Full Name: C-C motif chemokine ligand 20provided by RGD
Primary source: RGD:3646
See related: EnsemblRapid:ENSRNOG00000015992 AllianceGenome:RGD:3646
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: ST38; Scya20
Summary: Enables chemokine activity. Involved in cellular response to molecule of bacterial origin; chemotaxis; and positive regulation of macromolecule biosynthetic process. Located in extracellular space. Used to study transient cerebral ischemia. Biomarker of brain ischemia and ulcerative colitis. Orthologous to human CCL20 (C-C motif chemokine ligand 20). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 24.8), Thymus (RPKM 15.2) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q35

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (91837139..91839736)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (84389031..84391629)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (88918359..88921017)

Chromosome 9 - NC_086027.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ginkgolide B could alleviate MI/RI-induced inflammatory response through A20-NF-kappaB signal pathway, which may give us new insights into the preventive strategies for myocardial ischemia/reperfusion injury disease.
Title: Cardioprotection of Ginkgolide B on Myocardial Ischemia/Reperfusion-Induced Inflammatory Injury via Regulation of A20-NF-κB Pathway.
The results suggest a potential mechanism for the recruitment of IL-17-producing cells to degenerated intervertebral discs via a CCL20/CCR6 axis in vivo.
Title: Production of CCL20 on nucleus pulposus cells recruits IL-17-producing cells to degenerated IVD tissues in rat models.
Data show that systemic inflammatory reaction to raumatic brain injury starts before local brain response and suggest that CCL20 might play a role in promoting neuronal injury and central nervous system inflammation in response to mild TBI.
Title: Lateral fluid percussion injury of the brain induces CCL20 inflammatory chemokine expression in rats.
These findings suggest that MIP-3alpha/Ccl20 plays a pivotal role in inflammatory cascades in ischemic brains, and may be a novel therapeutic target for cerebral ischemia.
Title: Macrophage inflammatory protein-3alpha plays a key role in the inflammatory cascade in rat focal cerebral ischemia.
the role of TGF beta 1 in high glucose-induced MIP-3 alpha expression
Title: High glucose induces macrophage inflammatory protein-3 alpha in renal proximal tubule cells via a transforming growth factor-beta 1 dependent mechanism.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables CCR6 chemokine receptor binding	ISO Inferred from Sequence Orthology more info
enables CCR6 chemokine receptor binding	ISS Inferred from Sequence or Structural Similarity more info
enables chemokine activity	IDA Inferred from Direct Assay more info	PubMed
enables chemokine activity	IEA Inferred from Electronic Annotation more info
enables cytokine activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in T cell migration	ISO Inferred from Sequence Orthology more info
involved_in T cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide	ISO Inferred from Sequence Orthology more info
involved_in calcium-mediated signaling	ISO Inferred from Sequence Orthology more info
involved_in calcium-mediated signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to lipoteichoic acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of T cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-1 alpha production	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in regulation of T cell cytokine production	ISO Inferred from Sequence Orthology more info
NOT involved_in regulation of T-helper 17 cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info
involved_in thymocyte migration	ISO Inferred from Sequence Orthology more info
involved_in thymocyte migration	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: C-C motif chemokine 20

Names: CC chemokine LARC; CC chemokine ST38; MIP-3-alpha; beta-chemokine exodus-1; chemokine (C-C motif) ligand 20; liver and activation-regulated chemokine; macrophage inflammatory protein 3 alpha; small inducible cytokine subfamily A20; small-inducible cytokine A20

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_019233.2 → NP_062106.1 C-C motif chemokine 20 precursor

See identical proteins and their annotated locations for NP_062106.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

P97884

UniProtKB/TrEMBL

A6JWB9

Conserved Domains (1) summary

cd01119
Location:29 → 90

Chemokine_CC_DCCL; subgroup of the Chemokine_CC subgroup based on the presence of a DCCL motif involving the two N-terminal cysteine residues; includes a number of small inducible cytokines capable of reversibly inhibiting normal hematopoietic progenitor proliferation by ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086027.1 Reference GRCr8

Range

91837139..91839736

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006245164.5 → XP_006245226.1 C-C motif chemokine 20 isoform X1

UniProtKB/TrEMBL

A0A8L2QAZ9

Related

ENSRNOP00000021730.2, ENSRNOT00000021730.5

Conserved Domains (1) summary

cd01119
Location:28 → 89

Chemokine_CC_DCCL; Chemokine_CC_DCCL: subgroup of the Chemokine_CC subgroup based on the presence of a DCCL motif involving the two N-terminal cysteine residues; includes a number of small inducible cytokines capable of reversibly inhibiting normal hematopoietic ...